From ebf67f5fada2e8f536ac22d4de3cec98f50548da Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Wed, 10 Sep 2014 14:37:33 -0400
Subject: [PATCH] Fix references to config.ucsc_display_sites that I missed.

---
 display_applications/ucsc/bam.xml             | 2 +-
 display_applications/ucsc/bigbed.xml          | 2 +-
 display_applications/ucsc/bigwig.xml          | 2 +-
 display_applications/ucsc/interval_as_bed.xml | 2 +-
 display_applications/ucsc/maf_customtrack.xml | 2 +-
 display_applications/ucsc/vcf.xml             | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/display_applications/ucsc/bam.xml b/display_applications/ucsc/bam.xml
index a02a47e153f..29fd16720da 100644
--- a/display_applications/ucsc/bam.xml
+++ b/display_applications/ucsc/bam.xml
@@ -6,7 +6,7 @@
         <dynamic_param name="ucsc_link" value="1"/>
         <dynamic_param name="builds" value="2" split="True" separator="," />
         <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.ucsc_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('ucsc')}</filter>
         <filter>${dataset.dbkey in $builds}</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
         <url>${ucsc_link}db=${qp($bam_file.dbkey)}&amp;hgt.customText=${qp($track.url)}</url>
diff --git a/display_applications/ucsc/bigbed.xml b/display_applications/ucsc/bigbed.xml
index c9fe16b1bd3..4f5a284b725 100644
--- a/display_applications/ucsc/bigbed.xml
+++ b/display_applications/ucsc/bigbed.xml
@@ -6,7 +6,7 @@
         <dynamic_param name="ucsc_link" value="1"/>
         <dynamic_param name="builds" value="2" split="True" separator="," />
         <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.ucsc_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('ucsc')}</filter>
         <filter>${dataset.dbkey in $builds}</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
         <url>${ucsc_link}db=${qp($bigbed_file.dbkey)}&amp;hgt.customText=${qp($track.url)}</url>
diff --git a/display_applications/ucsc/bigwig.xml b/display_applications/ucsc/bigwig.xml
index ceaac487de3..779448af8aa 100644
--- a/display_applications/ucsc/bigwig.xml
+++ b/display_applications/ucsc/bigwig.xml
@@ -6,7 +6,7 @@
         <dynamic_param name="ucsc_link" value="1"/>
         <dynamic_param name="builds" value="2" split="True" separator="," />
         <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.ucsc_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('ucsc')}</filter>
         <filter>${dataset.dbkey in $builds}</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
         <url>${ucsc_link}db=${qp($bigwig_file.dbkey)}&amp;hgt.customText=${qp($track.url)}</url>
diff --git a/display_applications/ucsc/interval_as_bed.xml b/display_applications/ucsc/interval_as_bed.xml
index 2f74521f008..655bdf1a98a 100644
--- a/display_applications/ucsc/interval_as_bed.xml
+++ b/display_applications/ucsc/interval_as_bed.xml
@@ -6,7 +6,7 @@
         <dynamic_param name="ucsc_link" value="1"/>
         <dynamic_param name="builds" value="2" split="True" separator="," />
         <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.ucsc_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('ucsc')}</filter>
         <filter>${dataset.dbkey in $builds}</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
         <url>${ucsc_link}db=${qp($bed_file.dbkey)}&amp;position=${position.qp}&amp;hgt.customText=${bed_file.qp}</url>
diff --git a/display_applications/ucsc/maf_customtrack.xml b/display_applications/ucsc/maf_customtrack.xml
index 42be48b981f..0961a2f1c0d 100644
--- a/display_applications/ucsc/maf_customtrack.xml
+++ b/display_applications/ucsc/maf_customtrack.xml
@@ -6,7 +6,7 @@
         <dynamic_param name="ucsc_link" value="1"/>
         <dynamic_param name="builds" value="2" split="True" separator="," />
         <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.ucsc_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('ucsc')}</filter>
         <filter>${dataset.dbkey in $builds}</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
         <url>${ucsc_link}db=${qp($maf_customtrack_file.dbkey)}&amp;position=${maf_customtrack_file.metadata.vp_chromosome}:${maf_customtrack_file.metadata.vp_start}-${maf_customtrack_file.metadata.vp_end}&amp;hgt.customText=${maf_customtrack_file.qp}</url>
diff --git a/display_applications/ucsc/vcf.xml b/display_applications/ucsc/vcf.xml
index 715d9d81df4..d8f499e0edc 100644
--- a/display_applications/ucsc/vcf.xml
+++ b/display_applications/ucsc/vcf.xml
@@ -6,7 +6,7 @@
         <dynamic_param name="ucsc_link" value="1"/>
         <dynamic_param name="builds" value="2" split="True" separator="," />
         <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.ucsc_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('ucsc')}</filter>
         <filter>${dataset.dbkey in $builds}</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
         <url>${ucsc_link}db=${qp($bgzip_file.dbkey)}&amp;hgt.customText=${qp($track.url)}</url>